Hello all, I just wanted to share this problem with you in the event that anybody else encounters this and needs a quick solution. This is only half a solution because I don't have quite enough expertise to explain what caused it.
I was tasked with the job of cutting down a music video, provided as a ProRes 422. In Premiere CC 2014, using a sequence that matched the source settings, and exporting a ProRes, again matching the sequence settings and with maximum render quality enabled; but the result was a pixelated image, with jagged diagonal lines and a loss of image detail. In my years of editing I have never come across this - as far as I know the process should be lossless but it clearly wasn't.
I figured Premiere was the issue so I transferred my project to FCP7 and did the same thing, with the same result. It just so happens that this was the first time I have been editing at home for a paid gig, and I was worried that my laptop (MacBook Pro mid 2010 running Yosemite) might be the issue, as I am all too aware of the graphics cards issues associated with macbooks of that generation.
Solution: After reading a little about anti-aliasing issues with ProRes 422 (it is beyond my capabilities to explain those issues here), I transcoded my source file to a ProRes 4444, did the same cut in a 4444 sequence and kicked out an export with the same settings. Voila! Gave the client a very nicely compressed h264 which had no pixelation/aliasing issues. Unfortunately a couple of hours later than they wanted it.
Yet I'm still confused. Again, the purpose of this post is to suggest the 4444 route as a quick fix to the problem if anyone else encounters it. But if anyone has any better understanding of what might caused it, or a more efficient way of solving it then I would be really interested to hear.